Macromolecular interactions are central to cellular regulation and biological function, and antibody-antigen complexes are often used as a paradigms for molecular recognition. Protein-protein interactions are studied utilizing monoclonal antibodies (mAbs) specific for hen egg white lysozyme, a protein which has long served as a prototype for investigating the specificity of immune recognition. mAbs HH10, HH26, HH63, and HH8 recognize highly coincident epitopes and share over 90% sequence homology, but they differ significantly in their specificity properties. Differences in overall sensitivity of the 3 mAbs to mutations in the antigen epitope reflect differences among them in the relative stabilities of their association and dissociation rate constants, studied using surface plasmon resonance, to antigenic variation. HH8, the most cross-reactive, has fast on rates and slow off rates, and both rates are quite insensitive to antigenic variation. In contrast, both rates of HH26, the Ab whose sequence is most similar to that of the germ line genes, are sensitive to antigenic variation: mutations in the antigen both slow on rates and increase off rates. The structurally defined HH10 is intermediate in antigen sensitivity, with stable on rates but variable off rates. There are significant correlations between the intramolecular contacts, hydrophobicity, CDR flexibility, kinetics, and specificity of these 3 mAbs. The antibodies have been expressed as Fab in E. coli, and chain and domain swaps made. Results from the chimeric antibodies support the hypothesis that the stable on rate of HH8 correlates with H2, which is much more hydrophobic than H2 of the other antibodies, while differences among off-rates stabilities correlate with only a few residues in the L chains. Results with site-directed mutations support the hypothesis that specificity and affinity are significantly modulated by intramolecular salt link networks involving noncontact residues. We hypothesize that these salt link networks are largely responsible for conformational flexibility differences among the antibodies, which in turn modulate specificity and affinity. Thus, important structural differences among the 3 mAbs which determine the functional differences involve indirect, long-range effects by noncontact residues. It has been proposed that this type of conformational modulation may play an important role in antibody affinity maturation. A second antibody-antigen model, monoclonal antibodies to the carbohydrate O-antigen of Shigella flexnerii are similar to the anti-HEL mAbs, in that minimal, apparently conservative changes in structure cause significant differences in specificity and affinity properties. This a pattern of emergent properties which is of general significance to molecular recognition and directly applicable to rational design of vaccines and of antibodies with predefined specificity and functional properties. The Fabs of four mAbs with differing patterns of serotype cross-reactivity have been expressed in E. coli, and chimeric antibodies have been made to determine which of the limited structural differences among the Abs are responsible for the specificity differences among them.